I've given a lot of thought to the way I set up my Windows 7 system and it is based on some ideas that evolved through the years.
I built my system based on several themes: I wanted to have a lot of SATA ports and two PCIe ports. One PCIe for graphics, the other for an SSD (eventually when they come down in price).
I wanted to use as many drives as possible to allow for parallelism in drive access - most of the time the computer is waiting for the drive head to move to a spot, so if you can use more drives, they can seek in parallel.
Then again, you want to move as much write activity from your SSD as possible to avoid it's write cycle lifespan problems.
But I don't have an SSD yet.
Here is the way I have set things up:
Each of these disks are 2TB drives, Disk 2 and 5 are Sata 600, the others are Sata 300. Disk 0 and 1 are external, the rest are internal. Disk 6 is a USB thumb drive which is formatted in NTFS because I use encryption and compression on it.
Disk 0 is solely used by Retrospect for nightly incremental file backup. It is an external drive, but I keep it attached all the time.
Disk 1 is solely used by Acronis for full image backups. It is also an external drive, but I keep it attached all the time. I only make image backups when I have made some major changes.
Disk 2 is a high-speed SATA 600 drive with the System partition and program files. It also has a G: partition that I use to save private stuff.
Disk 3 has the TMP partition which has the swap file, TEMP folder location, internet cache files and stuff like that. The second partition on it is called 'Big Boy 1' and it has all my software installations and various large files. It is my 'garage' or 'attic' - a repository for stuff and a lot of junk. I don't back it up because it's too big.
Disk 4 has a Big Boy 2 partition that is a copy of Big Boy 1 - copied because I don't back this up. I use ROBOCOPY scripts to keep them in sync. The TMP2 folder is used for Windows Search and some other scratch stuff.
Disk 5 is a high-speed SATA 600 drive with two partitions: 'Jim' contains my desktop, email, document, etc. - the various user folders. 'Komplete' has all my audio projects and samples and libraries.
Disk 6 is a mini-usb drive that is only about 1/4 inch long on the outside - it plugs into an external USB 2 slot on the front panel. It is encrypted and compressed. It holds my security info, KeePass stuff, scripts, BOOT Prom images, a few ISO boot images, and miscellaneous disaster recovery files.
This, I suppose is rather elaborate, and I tend to monitor file system things in detail, while I imagine most don't want to think too much about files and directory locations.